Hi C.Wolfe,
Your suggestion may be possible, and it somewhat makes sense to me, however I am not sure this would work for Mike's current procedures. The main issue here, is that these screens have been designed so you can only make payments on Invoices, the "Receive Payments" screen from within Method only accepts payments for invoices as well. Technically it would be possible to remove this limitation by Customizing your payment screens from within Method, however I can't say for sure if this would cause any other problems down the line when syncing with your QuickBooks account.
Mike has been using the Method in-house Consulting Services, so I did speak with his Consulatant, and they believe this should be possible, however they still need to get this implemented before we can say for sure.
-Ben